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MFM > DNA Replication and Repair > Flashcards

DNA Replication and Repair Flashcards

1
Q

What is the normal glutamine repeat allowance?

A

less than 28 CAG repeats

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2
Q

what is an insertion?

A

extra nucleotide is added, and can change the reading frame and cause a FRAMESHIFT mutation

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3
Q

what is heterochromatin?

A

condensed dna in the center or end of a chromosome

no expressed genes

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4
Q

what is primase?

A

RNA polymerase, it synthesizes a short RNA primer with a 3’ OH group

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5
Q

third step of base excision repair?

A

DNA polymerase fills in the gap

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6
Q

What is the reaction of the replication machinery to depurination?

A

the machinery can skip to the next complete nucleotide, producing a nucleotide deletion in the newly synthesized strand

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7
Q

what is FEN1?

A

flap endonuclease 1 -processes the 5’ end of Okazaki fragments to allow for ligation - removes 5’ “flaps” that hang off d/t unpaired bases

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8
Q

What sequences are repeated usually in telomeres?

A

TTAGGG

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9
Q

function of Ku70/80

A

acts as a scaffold on the ends of the broken DNA, guides DNA-PKcs to broken ends, protects ends from further degradation

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10
Q

what is the function of helicase?

A

sits at the front of the replication fork and uses energy of ATP hydrolysis to propel itself forward and pry open DNA double helix

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11
Q

what proteins are involved in nonhomologous end joining?

A

Ku70/80 (scaffold on the ends of the broken DNA, guides DNA-PKcs to broken ends, protects ends from further degradation)

DNA-PKcs (DNA dependent protein kinase catalytic subunit)

These two join together to make fully active DNA-PK

MRN, CtIP, artemis, ligase 4, XRCC4, XLF

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12
Q

what is RFC?

A

replication factor C - clamp loader protein - recognizes the single strand DNA binding protein (RPA) loads the clamp PCNA so that the front is oriented toward 3’ end (where dna pol delta will associate with PCNA)

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13
Q

large difference between NHEJ and homologous recombination?

A

NHEJ is prone to further mutation and error, homologous recombination is error free (it requires a homologous chromosome to be used as a template)

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14
Q

What is the function of DNA polymerase alpha?

A

it is complexed with primase to start the primer - initiates lagging strand synthesis

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15
Q

steps of the homologous recombination method

A
  1. 2 homologous chromosomes become aligned
  2. nuclease generates single stranded ends at the break (chews back one of the complementary strand)
  3. one of the single strands invades homologous DNA duplex by forming base pairs with complementary strand (makes a branch point where one strand from each duplex crosses) (makes a D loop comprised of overhanging 3’ invader and homologous chromosome)
  4. invading strand elongated by DNA polymerase, using the complementary strand as a template
  5. branch point migrates as base pairs holding together duplexes break and new ones form
  6. add’l dna synthesis and ligation complete repair
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16
Q

what does histone acetyltransferase do??

A

adds an acetyl group to lysine on the amino terminal tail of the histone

removes the positive charge and WEAKENS the bond between histone and DNA

therefore, opens region in dna for regulatory proteins to bind and increases gene expression

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17
Q

what does the thymidine analog of AZT do in DNA?

A

replaces thymidine during dna synthesis, therefore terminates the dna chain since there is no 3’ OH to add more nucleotides onto

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18
Q

what proteins are involved with mismatch repair?

A

proteins start with “MSH” or “MLH” the mismatch repair enzyme complex recognizes error, removes the segment with the mismatch, and DNA polymerase and ligase repair gap

ex. MSH6, MSH2, MLH1

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19
Q

which proteins are involved with excision repair?

A

these repair proteins start with XP - they recognize damage done to the DNA

ex. XPA, XPC, XPG, ETC

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20
Q

what end does DNA polymerase add nucleotides to?

A

3’ (3’ OH reacts with phosphate of incoming nucleotide)

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21
Q

2 general types of single nucleotide defect repair?

A

nucleotide excision repair and base excision repair, and mismatch repair

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22
Q

info about acyclovir?

what does this analog replace?

A

replaces guanosine triphosphate

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23
Q

third step of nucleotide excision repair?

A

newly sythesized segment is joined to 5’ end of remainder of original DNA strand by DNA ligase

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24
Q

what would occur if the mutation went unrepaired?

A
  1. substitution of base pair would be inserted (may be incorrect) 2. deletion of nucleotide pairs 3. stall of DNA replication (thymine dimer)
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25
Q

first step of nucleotide excision repair?

A

specific repair endonucleases cleave the abnormal chain and remove damaged region

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26
Q

pathology of Zellweger syndrome

A

mutations of peroxins (the proteins involved in formation of peroxisomes), leading to the accumulation of very long chain fatty acids

clinical characteristics: impaired brain development, liver and kidney lesions, and elevated very long chain fatty acids in the blood

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27
Q

when is mismatch repair performed?

A

REPLICATION ERROR: during DNA replication when an incorrect but normal base is incorporated into the chain (not normal watson-crick base pair) - there is a physical bulge that is recognized

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28
Q

what is depurination?

A

removing the purine base from a nucleotide (an OH is left in its place)

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29
Q

what is euchromatin?

A

contains expressed genes, is less condensed and more extended

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30
Q

what is the specific function of ATM?

A

is recruited by the MRN complex that recognizes the break, and activates P53.

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31
Q

Pathology of Tay-Sachs?

A

deficiency of hexosaminidase A in the lysosome, enzyme deficiency causes accumulation of gangliosides in the neurons, resulting in neuronal cell death

characterized by cherry red spot on retina

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32
Q

what is PCNA?

A

THE SLIDING CLAMP proliferating cell nuclear antigen, it is a DNA clamp that is a processivity factor for DNA pol delta, it encircles the dna and allows the polymerase to stay attached to DNA for longer amt of time

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33
Q

2 types of repair for double stranded breaks in DNA?

A

nonhomologous end joining and homologous recombination

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34
Q

What is a missense mutation?

A

results in codon that codes for a different amino acid

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35
Q

pathology of progeria

A

mutation in nuclear lamina gene Lamin A

causes cryptic splice site that mutates the final protein form into progerin.

progerin is not properly integrated into the lamina, causing a disfigured nucleus and altered genomic integrity

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36
Q

what is the cause of trinucleotide expansions?

A

slippage during DNA replication 1. newly synth strand dissociates from template strand 2. kink is formed 3. repeat sequences allow new strand to re-anneal in the wrong location, creating a duplication of that region

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37
Q

what is the function of P53

A

arrests the cell and gives it time to repair and recruit the proteins for repair, can also induce apoptosis

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38
Q

2 general causes of DNA mutations?

A

spontaneous, induced

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39
Q

what direction can DNA polymerase move in? ONLY

A

5-3

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40
Q

why can azidothymidine (AZT) treat retroviral infections?

A

the viral enzyme reverse transcriptase uses AZT triphosphate preferentially over cellular thymidine triphospate

41
Q

what step occurs after the break recognition and resection in homologous recombination repair?

A

RPA coats the single strand DNA on the 3’ end, which summons Rad51 and Brca2. then Rad52 and Rad 54 load and these find identical DNA duplex and invade the sister chromatid

42
Q

function of alpha-L-iduronidase

A

breaks down glycosaminoglycans

43
Q

what is the function of Brca2?

A

binds the single strand DNA and directly interacts with the recombinase RAD51 to stimulate and maintain strand invasion

44
Q

what proteins recognize double strand DNA breaks? and what do they do?

A

ATM, MRN complexes, nucleases

these recognize the break and begin to resect the 5’ end from the break

45
Q

what is the most common mechanism for repairing double strand breaks in somatic cells?

A

non homologous end joining

46
Q

characteristic of non homologous end joining vs homologous end joining?

A

NHEJ does not require a homologous chromosome as a template, so there may be mutations introduced

47
Q

What is the cause of xeroderma pigmentosum?

A

the failure to repair thymine dimers after UV radiation exposure

48
Q

what proteins bind to the exposed single DNA strands to keep the base pairs from coming back together? What is an example of one?

A

single strand binding proteins (SSB’s) RPA

49
Q

pertinent information about acyclovir:

analog of what?

A

guanosine

50
Q

which cells do not experience telomere shortening?

A

germ and stem cells

51
Q

what is the function of dna polymerase epsilon?

A

leading strand synthesis

52
Q

What binds to the ORC/MCM complex after they come together?

A

helicase - begins separating strands to form replication bubble

53
Q

function of DNA-PKcs

A

finds Ku protein at the end of broken strands and forms DNA-PK active complex (kinase activity)

54
Q

what are translocations?

A

a gross chromosomal rearrangement resulting from breaks in chromosomes, when the free ends of the DNA at the break points reseal with the free ends of a different broken chromosome

55
Q

function of hexosaminidase A

A

breaks down ganglioside in the brain

56
Q

what is the pathophysiology of xeroderma pigmentosum?

A

there is a defect in the nucleotide excision repair due to mutation in XP genes (XPA, XPB, XPC, XPD), so NER cannot remove UV damaged thymine dimers (or bases) and there is an accumulation of mutations

57
Q

what are the 2 major types of DNA damage that absolutely need repair?

A

single nucleotide defects and double stranded breaks in DNA

58
Q

when is base excisision repair specificlaly used?

A

it is used to correct spontaneous mutations introduced during replications due to deaminations and depurinations

59
Q

pathology of Hurler syndrome

A

defect in alpha-L-iduronidase, resulting in accumulation of undigested glycosaminoglycans (GAGs) in the lysosome

clinically characterized by skeletal abnormalities, mental retardation, and nondegraded GAGs in urine

60
Q

which cancer/syndrome is associated with mutations in mismatch repair proteins?

A

hereditary nonpolyposis colorectal cancer

Lynch Syndrome

61
Q

what is a deletion?

A

loss of nucleotide, can change reading frame to result in frameshift mutation

62
Q

why is acyclovir used to treat retroviral infections

A

retroviral thymidine kinase can convet the analog nucleoside into a nucleotide more efficiently

63
Q

What is the function of the ORC?

A

origin recognition complex, binds to origin and recruits MCM

64
Q

2 steps of nonhomologous end joining

A
  1. nucleases process the broken ends to form blunt ends (nucleotides are lost)
  2. the ends are brought together by enzymes and rejoined by DNA ligase
65
Q

second step of base excision repair?

A

endonuclease cleaves the sugar phosphate strand at the site where the sugar phosphate backbone backs a base

66
Q

when can homologous recombination occur in the cell cycle?

A

G2 and M phase, after replication

this is because the sister chromatids must be present (not prior to S phase)

67
Q

second step of nucleotide excision repair?

A

gap made by first step is filled by DNA polymerase that adds deoxyribonucleotides one at a time to 3’, using intact complementary DNA strand as template

68
Q

what pathway is defective in people with ataxia telangiectasia?

A

defective NHEJ and homologous recombination repair due to mutation in ATM

and are susceptible to agents that cause double stranded breaks

69
Q

what is deamination?

A

spontaneous loss of an amino group from a cytosine, making the nitrogenous base a URACIL instead (O instead of NH2)

70
Q

pathology of Lynch Syndrome?

A

mutations in MSH2 or MLH1

  • the cells are unable to repair nucleotide mismatches
  • afflicted person at increased risk for cancer
71
Q

what is the reaction of the replication machinery to deamination?

A

machinery inserts an adenine when it encounters the uracil on the template strand

72
Q

first step of base excision repair?

A

DNA glycosylase cleaves the N-glycosidic bond that joins that damaged base to the deoxyribose

73
Q

what is AZT (azidothymidine) an analog of?

A

thymidine (has amino group instead of 3’ OH)

74
Q

fourth step of base excision repair?

A

DNA ligase joins newly synthesized segment to the original DNA strand

75
Q

what is a nonsense mutation?

A

results in a premature stop codon

76
Q

when is nucleotide excision repair specifically used?

A

to removal thymine dimers and bulky adducts

77
Q

what is the function of dna polymerase delta?

A

lagging strand synthesis

78
Q

what is DNA ligase?

A

joins the 5’ phosphate end of one new DNA frag to the adjacent 3’ hydroxyl end of the next (fills in the gaps left by RNA primer removal) (makes a phosphodiester bond)

79
Q

what does histone deacetylase do?

A

removes acetyl group from lysine tail, makes it more positive and increases the bonding of histones to dna, thus increasing condensation of dna and decreasing levels of gene expression

80
Q

mechanism of benzo(a)pyrene induced mutation?

A

HIGHLY mutagenic, when oxidized by cytochrome P450, it forms bulky adducts with guanine residues in DNA

81
Q

what does ultraviolet radiation do to DNA?

A

promotes covalent link between two pyrimidine bases forming pyrimidine (thymine) dimers

82
Q

what stage does nonhomologous end joining occur in?

A

stage G1, when the cells are not in replication anymore

83
Q

info about acyclovir:

what does this analog contain?

A

open chain structure instead of sugar molecule

84
Q

types of point mutations?

A
  1. missense 2. nonsense 3. insertion/deletion
85
Q

what is telomerase used for?

A

extends the DNA template to give space for RNA primer to be added for full replication - therefore, telomerase contains both proteins and RNA template (complimentary sequence to repeating sequence in telomere) IS A RNA-DEPENDENT DNA POLYMERASE

86
Q

types of mutations?

A
  1. point mutations 2. trinucleotide expansions 3. chromosomal translocations
87
Q

What is the function of topoisomerase?

A

make transient nicks in DNA backbone (phosphodiester bond of ONE strand) to relieve supercoiling, they reseal the DNA before falling off

88
Q

What is Huntington’s Disease caused by, and what are the indicators?

A

trinucleotide expansion in the gene encoding protein huntingtin, when there are more than 40 CAG repeats (glutamine)

89
Q
A
90
Q

mechanism of xray induced mutation?

A

xray excites water in the cells, leading to hydroxyl radicals, which react with DNA, which alters the structure of the bases or cleaves the DNA strands (double strand break)

91
Q

What is the function of the MCM?

A

binds to the ORC, unwinds double stranded DNA at these origins (helicase), recruits DNA polymerase, and initiates DNA asynthesis

92
Q

what causes double stranded DNA breaks usually?

A

exposure to ionizing radiation (xrays and radioactive material)

93
Q

what is RNAseH?

A

ribonuclease H, is an endoribonuclease that hydrolyzes the phosphodiester bonds of RNA when hybridized to DNA (aka cleaves RNA primer from the 5’ ends of okazaki fragments in a DNA/RNA hybrid) - does not digest single or double stranded DNA

94
Q

correlation between cancer cells and telomeres?

A

cancer cells upregulate telomere activity and INCREASE the length of the telomere, adding to the immortality of cancer cells

95
Q

what mutation do individuals with ataxia telangiestasia have?

A

mutation in ATM, so they have an impaired DNA damage response

96
Q

which mutations can cause frameshift mutations?

A

insertions and deletions

97
Q

what cancers are people with lynch syndrome more likely to develop? (8)

A

colorectal, endometrial, stomach, ovarian, ureter, brain, hepatobiliary tract, skin

98
Q

what proteins are involved in NHEJ?

A

Ku70/80, DNA-PKcs, DNA-PK, MRN

99
Q

proteins involved in homologous recombination?

A

ATM, MRN, nuclease, RPA, BRCA2, RAD51/52, p53

MFM (39 decks)

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